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Complex (mhc i/peptide) PDB id
1bii
Jmol
Contents
Protein chains
274 a.a. *
99 a.a. *
Ligands
ARG-GLY-PRO-GLY-
ARG-ALA-PHE-VAL-
THR-ILE
Waters ×65
* Residue conservation analysis
PDB id:
1bii
Name: Complex (mhc i/peptide)
Title: The crystal structure of h-2dd mhc class i in complex with the HIV-1 derived peptide p18-110
Structure: Mhc class i h-2dd. Chain: a. Fragment: heavy chain, extracellular domains. Synonym: dd. Engineered: yes. Beta-2 microglobulin. Chain: b. Engineered: yes. Decameric peptide.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.40Å     R-factor:   0.278     R-free:   0.323
Authors: A.Achour,K.Persson,R.A.Harris,J.Sundback,C.L.Sentman, Y.Lindqvist,G.Schneider,K.Karre
Key ref:
A.Achour et al. (1998). The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition. Immunity, 9, 199-208. PubMed id: 9729040 DOI: 10.1016/S1074-7613(00)80602-0
Date:
11-Jun-98     Release date:   14-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01900  (HA12_MOUSE) -  H-2 class I histocompatibility antigen, D-D alpha chain
Seq:
Struc: 		365 a.a.
274 a.a.
Protein chain
Pfam   ArchSchema ?
P01887  (B2MG_MOUSE) -  Beta-2-microglobulin
Seq:
Struc: 		119 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     immune response   2 terms 

 

 
DOI no: 10.1016/S1074-7613(00)80602-0 Immunity 9:199-208 (1998)
PubMed id: 9729040  
 
 
The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition.
A.Achour, K.Persson, R.A.Harris, J.Sundbäck, C.L.Sentman, Y.Lindqvist, G.Schneider, K.Kärre.
 
  ABSTRACT  
 
The structure of H-2Dd complexed with the HIV-derived peptide P18-I10 (RGPGRAFVTI) has been determined by X-ray crystallography at 2.4 A resolution. This MHC class I molecule has an unusual binding motif with four anchor residues in the peptide (G2, P3, R/K/H5, and I/L/F9 or 10). The cleft architecture of H-2Dd includes a deep narrow passage accomodating the N-terminal part of the peptide, explaining the obligatory G2P3 anchor motif. Toward the C-terminal half of the peptide, p5R to p8V form a type I' reverse turn; residues p6A to p9T, and in particular p7F, are readily exposed. The structure is discussed in relation to functional data available for T cell and natural killer cell recognition of the H-2Dd molecule.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic View of the H-2D^d ComplexThe α and β chains are depicted in red and blue, respectively. The bound P18-I10 decapeptide is shown in a ball and stick representation. The figure was created using the Molscript program ([36]). 		Figure 4.
Figure 4. Interaction of the GP Anchor Motif in the Binding Cleft(A) p2G is the only amino acid that fits in the narrow passage between R66 and Y159. The van der Waals surfaces of R66 and Y159 are colored in blue, while the van der Waals surface of p2G is colored in gray (section across the cleft, viewed from the C terminus of the peptide).(B) The side chain of p3P is situated in a hydrophobic pocket formed by the side chains of V9, W97, A99, W114, and Y159 that stacks with its aromatic ring to p3P. The carbonyl of p3P binds through hydrogen bonds (depicted as broken lines) to the side chains of R66 and N70. The figure was created using the Grasp program ([49]). The color of the atoms is red for oxygen, blue for nitrogen, and white for carbon.
 
  The above figures are reprinted by permission from Cell Press: Immunity (1998, 9, 199-208) copyright 1998.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19625641 R.Wang, K.Natarajan, and D.H.Margulies (2009).
Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position.
  J Immunol, 183, 2554-2564.
PDB codes: 3dmm 3ecb
  18323608 W.Chen, F.Chu, H.Peng, J.Zhang, J.Qi, F.Jiang, C.Xia, and F.Gao (2008).
Expression, purification, crystallization and preliminary X-ray diffraction analysis of grass carp beta2-microglobulin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 200-202.  
17208967 Y.Nakagawa, H.Kikuchi, and H.Takahashi (2007).
Molecular analysis of TCR and peptide/MHC interaction using P18-I10-derived peptides with a single D-amino acid substitution.
  Biophys J, 92, 2570-2582.  
16365312 J.J.Credle, J.S.Finer-Moore, F.R.Papa, R.M.Stroud, and P.Walter (2005).
On the mechanism of sensing unfolded protein in the endoplasmic reticulum.
  Proc Natl Acad Sci U S A, 102, 18773-18784.
PDB code: 2be1
16089503 R.Olson, K.E.Huey-Tubman, C.Dulac, and P.J.Bjorkman (2005).
Structure of a pheromone receptor-associated MHC molecule with an open and empty groove.
  PLoS Biol, 3, e257.
PDB code: 1zs8
16181330 T.H.Hansen, L.Lybarger, L.Yu, V.Mitaksov, and D.H.Fremont (2005).
Recognition of open conformers of classical MHC by chaperones and monoclonal antibodies.
  Immunol Rev, 207, 100-111.  
15699351 Y.Wang, A.Rubtsov, R.Heiser, J.White, F.Crawford, P.Marrack, and J.W.Kappler (2005).
Using a baculovirus display library to identify MHC class I mimotopes.
  Proc Natl Acad Sci U S A, 102, 2476-2481.  
15213391 C.Kellenberger, S.Porciero, and A.Roussel (2004).
Expression, refolding, crystallization and preliminary crystallographic study of MHC H-2Kk complexed with octapeptides and nonapeptides.
  Acta Crystallogr D Biol Crystallogr, 60, 1278-1280.  
14555655 R.C.Hillig, M.Hülsmeyer, W.Saenger, K.Welfle, R.Misselwitz, H.Welfle, C.Kozerski, A.Volz, B.Uchanska-Ziegler, and A.Ziegler (2004).
Thermodynamic and structural analysis of peptide- and allele-dependent properties of two HLA-B27 subtypes exhibiting differential disease association.
  J Biol Chem, 279, 652-663.
PDB code: 1jgd
15060000 R.D.Emes, S.A.Beatson, C.P.Ponting, and L.Goodstadt (2004).
Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents.
  Genome Res, 14, 591-602.  
14583622 Y.Samino, D.Lopez, S.Guil, P.de León, and M.Del Val (2004).
An endogenous HIV envelope-derived peptide without the terminal NH3+ group anchor is physiologically presented by major histocompatibility complex class I molecules.
  J Biol Chem, 279, 1151-1160.  
12454016 D.M.Hill, T.Kasliwal, E.Schwarz, A.M.Hebert, T.Chen, E.Gubina, L.Zhang, and S.Kozlowski (2003).
A dominant negative mutant beta 2-microglobulin blocks the extracellular folding of a major histocompatibility complex class I heavy chain.
  J Biol Chem, 278, 5630-5638.  
  12121655 J.Ding, A.D.Smith, S.C.Geisler, X.Ma, G.F.Arnold, and E.Arnold (2002).
Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1.
  Structure, 10, 999.
PDB code: 1k5m
12010576 P.E.Adrian, G.Rajaseger, V.S.Mathura, M.K.Sakharkar, and P.Kangueane (2002).
Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.
  BMC Struct Biol, 2, 2.  
11991985 P.K.Hocknell, R.D.Wiley, X.Wang, T.G.Evans, W.J.Bowers, T.Hanke, H.J.Federoff, and S.Dewhurst (2002).
Expression of human immunodeficiency virus type 1 gp120 from herpes simplex virus type 1-derived amplicons results in potent, specific, and durable cellular and humoral immune responses.
  J Virol, 76, 5565-5580.  
11148219 N.Matsumoto, M.Mitsuki, K.Tajima, W.M.Yokoyama, and K.Yamamoto (2001).
The functional binding site for the C-type lectin-like natural killer cell receptor Ly49A spans three domains of its major histocompatibility complex class I ligand.
  J Exp Med, 193, 147-158.  
11343276 T.K.Mandal, and C.Mukhopadhyay (2001).
Effect of glycosylation on structure and dynamics of MHC class I glycoprotein: a molecular dynamics study.
  Biopolymers, 59, 11-23.  
10934233 M.C.Nakamura, S.Hayashi, E.C.Niemi, J.C.Ryan, and W.E.Seaman (2000).
Activating Ly-49D and inhibitory Ly-49A natural killer cell receptors demonstrate distinct requirements for interaction with H2-D(d).
  J Exp Med, 192, 447-454.  
  11045629 O.Schueler-Furman, Y.Altuvia, A.Sette, and H.Margalit (2000).
Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles.
  Protein Sci, 9, 1838-1846.  
10607669 K.Maenaka, and E.Y.Jones (1999).
MHC superfamily structure and the immune system.
  Curr Opin Struct Biol, 9, 745-753.  
10429675 Q.R.Fan, and D.C.Wiley (1999).
Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor.
  J Exp Med, 190, 113-123.
PDB code: 1qqd
  10368281 R.Stanfield, E.Cabezas, A.Satterthwait, E.Stura, A.Profy, and I.Wilson (1999).
Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.
  Structure, 7, 131-142.
PDB codes: 1f58 2f58 3f58
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.